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Research Advances in Plant Genomics
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Research Advances in Plant Genomics

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Plant Science".

Deadline for manuscript submissions: closed (20 September 2021) | Viewed by 50596

Special Issue Editors

Dr. Jitendra Kumar

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Guest Editor
Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN 55108, USA
Interests: plant pathology; molecular biology; functional genomics; reverse genetics
Special Issues, Collections and Topics in MDPI journals
Dr. Krishan Mohan Rai

E-Mail Website
Guest Editor
Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
Interests: plant molecular biology; genomics and bioinformatics
Special Issues, Collections and Topics in MDPI journals
Dr. Praveen C. Verma

E-Mail Website
Guest Editor
Department of Molecular Biology and Biotechnology, CPMB Building, National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, UP, India
Interests: plant molecular biology; pest resistance; genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The new era of “Plant Genomics” research aims to understand the plant genetic and phenotypic development to accelerate crop improvement in challenging environmental conditions. Breeding efforts and improved pest management have helped in increased crop yields globally. However, the ever-increasing world population and shrinking farmland coupled with abiotic and biotic stresses threaten food insecurity for millions of people worldwide. The crop yield can be improved by increasing the number of grains produced per plant, the number of plants per unit area, and the size of grains. Plants genomics has demonstrated interesting insights into the mechanisms associated with growth, development, and stress responses and can be exploited for the achievement of the aforementioned traits by genetic changes.

This Research Topic aims to collect recent advances emphasizing the role of genomics in the selection and improvement of crop traits to meet the food requirements of the future. This Special Issue on plant genomics welcomes submissions of original research, reviews, or perspective articles addressing current technical advances in plant genomics aimed at connecting plant physiological processes with gene expression dynamics during growth and development of the plant, flowering and grain filling, and abiotic and biotic stresses. Manuscripts highlighting the use of comparative genome analysis, transcriptomics, small RNAs, and other novel coding and noncoding RNAs in plant research and describing future challenges are also welcome. Manuscripts utilizing advanced bioinformatics tools and databases toward enhancing the capabilities of existing plant genomics approaches for a better understanding of plant development are also encouraged for submission.

Dr. Jitendra Kumar
Dr. Krishan Mohan Rai
Dr. Praveen C. Verma
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • plant molecular biology
  • stress tolerance
  • disease resistance
  • trait improvement by genetic modifications
  • genome editing
  • plant genome sequencing
  • plant bioinformatics

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Published Papers (11 papers)

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Editorial

Jump to: Research, Review

3 pages, 159 KiB  
Editorial
Research Advances in Plant Genomics
by Jitendra Kumar and Krishan Mohan Rai
Life 2021, 11(12), 1313; https://doi.org/10.3390/life11121313 - 28 Nov 2021
Cited by 1 | Viewed by 1721
Abstract
Breeding efforts have helped in increasing crop yields globally [...] Full article
(This article belongs to the Special Issue Research Advances in Plant Genomics)

Research

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20 pages, 6911 KiB  
Article
Transcriptomic Analysis of Genes Involved in Plant Defense Response to the Cucumber Green Mottle Mosaic Virus Infection
by Anna Slavokhotova, Tatyana Korostyleva, Andrey Shelenkov, Vitalii Pukhalskiy, Irina Korottseva, Marina Slezina, Ekaterina Istomina and Tatyana Odintsova
Life 2021, 11(10), 1064; https://doi.org/10.3390/life11101064 - 10 Oct 2021
Cited by 14 | Viewed by 3039
Abstract
Plants have evolved a complex multilayered defense system to counteract various invading pathogens during their life cycle. In addition to silencing, considered to be a major molecular defense response against viruses, different signaling pathways activated by phytohormones trigger the expression of secondary metabolites [...] Read more.
Plants have evolved a complex multilayered defense system to counteract various invading pathogens during their life cycle. In addition to silencing, considered to be a major molecular defense response against viruses, different signaling pathways activated by phytohormones trigger the expression of secondary metabolites and proteins preventing virus entry and propagation. In this study, we explored the response of cucumber plants to one of the global pathogens, cucumber green mottle mosaic virus (CGMMV), which causes severe symptoms on leaves and fruits. The inbred line of Cucumis sativus L., which is highly susceptible to CGMMV, was chosen for inoculation. Transcriptomes of infected plants at the early and late stages of infection were analyzed in comparison with the corresponding transcriptomes of healthy plants using RNA-seq. The changes in the signaling pathways of ethylene and salicylic and jasmonic acids, as well as the differences in silencing response and expression of pathogenesis-related proteins and transcription factors, were revealed. The results show that silencing was strongly suppressed in infected plants, while the salicylic acid and ethylene signaling pathways were induced. The genes encoding pathogenesis-related proteins and the genes involved in the jasmonic acid pathway changed their expression insignificantly. It was also found that WRKY and NAC were the most sensitive to CGMMV infection among the transcription factors detected. Full article
(This article belongs to the Special Issue Research Advances in Plant Genomics)
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17 pages, 4415 KiB  
Article
Study of Triticum aestivum Resistome in Response to Wheat dwarf India Virus Infection
by Jitendra Kumar, Krishan Mohan Rai, Shahryar F. Kianian and Sudhir P. Singh
Life 2021, 11(9), 955; https://doi.org/10.3390/life11090955 - 13 Sep 2021
Cited by 2 | Viewed by 2497
Abstract
Susceptible and resistant germplasm respond differently to pathogenic attack, including virus infections. We compared the transcriptome changes between a resistant wheat cultivar, Sonalika, and a susceptible cultivar, WL711, to understand this process in wheat against wheat dwarf India virus (WDIV) infection. A total [...] Read more.
Susceptible and resistant germplasm respond differently to pathogenic attack, including virus infections. We compared the transcriptome changes between a resistant wheat cultivar, Sonalika, and a susceptible cultivar, WL711, to understand this process in wheat against wheat dwarf India virus (WDIV) infection. A total of 2760 and 1853 genes were differentially expressed in virus-infected and mock-inoculated Sonalika, respectively, compared to WL711. The overrepresentation of genes involved in signaling, hormone metabolism, enzymes, secondary metabolites, proteolysis, and transcription factors was documented, including the overexpression of multiple PR proteins. We hypothesize that the virus resistance in Sonalika is likely due to strong intracellular surveillance via the action of multiple PR proteins (PR1, RAR1, and RPM1) and ChiB. Other genes such as PIP1, LIP1, DnaJ, defensins, oxalate oxidase, ankyrin repeat protein, serine-threonine kinase, SR proteins, beta-1,3-glucanases, and O-methyltransferases had a significant differential expression and play roles in stress tolerance, may also be contributing towards the virus resistance in Sonalika. In addition, we identified putative genes with unknown functions, which are only expressed in response to WDIV infection in Sonalika. The role of these genes could be further validated and utilized in engineering resistance in wheat and other crops. Full article
(This article belongs to the Special Issue Research Advances in Plant Genomics)
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13 pages, 4870 KiB  
Article
Transcriptome Profiling Reveals Molecular Changes during Flower Development between Male Sterile and Fertile Chinese Cabbage (Brassica rapa ssp. pekinensis) Lines
by Jingfeng Hu, Mei Lan, Xuezhong Xu, Hongli Yang, Liqin Zhang, Fengxian Lv, Huiju Yang, Ding Yang, Chongjuan Li and Jiangming He
Life 2021, 11(6), 525; https://doi.org/10.3390/life11060525 - 4 Jun 2021
Cited by 8 | Viewed by 3573
Abstract
Male sterility exists widely in flowering plants and is used as a fascinating tool by breeders for creating hybrid varieties. Herein, stamen samples from male sterile CCR20000 and male fertile CCR20001 lines during two developmental stages were employed to elucidate the molecular changes [...] Read more.
Male sterility exists widely in flowering plants and is used as a fascinating tool by breeders for creating hybrid varieties. Herein, stamen samples from male sterile CCR20000 and male fertile CCR20001 lines during two developmental stages were employed to elucidate the molecular changes during flower development in fertile and sterile Chinese cabbage lines. RNA-seq revealed weak transcriptional activity in the sterile line, which may have led to the abnormal stamen development. The differentially expressed genes were enriched in plant hormone, carbon metabolism, and biosynthesis of amino acid pathways. Important genes with opposite patterns of regulation between the two lines have been associated with the male sterility trait. Members of the transcription factor families such as AP2, MYB, bHLH, and WRKY were highly active in the regulation of structural genes involved in pollen fertility. This study generated important genomic information to support the exploitation of the male sterility trait in Chinese cabbage breeding programs. Full article
(This article belongs to the Special Issue Research Advances in Plant Genomics)
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21 pages, 3019 KiB  
Article
Priming by High Temperature Stress Induces MicroRNA Regulated Heat Shock Modules Indicating Their Involvement in Thermopriming Response in Rice
by Akhilesh Kumar Kushawaha, Ambreen Khan, Sudhir Kumar Sopory and Neeti Sanan-Mishra
Life 2021, 11(4), 291; https://doi.org/10.3390/life11040291 - 29 Mar 2021
Cited by 26 | Viewed by 4825
Abstract
Rice plants often encounter high temperature stress, but the associated coping strategies are poorly understood. It is known that a prior shorter exposure to high temperature, called thermo-priming, generally results in better adaptation of the plants to subsequent exposure to high temperature stress. [...] Read more.
Rice plants often encounter high temperature stress, but the associated coping strategies are poorly understood. It is known that a prior shorter exposure to high temperature, called thermo-priming, generally results in better adaptation of the plants to subsequent exposure to high temperature stress. High throughput sequencing of transcript and small RNA libraries of rice seedlings primed with short exposure to high temperature followed by high temperature stress and from plants exposed to high temperature without priming was performed. This identified a number of transcripts and microRNAs (miRs) that are induced or down regulated. Among them osa-miR531b, osa-miR5149, osa-miR168a-5p, osa-miR1846d-5p, osa-miR5077, osa-miR156b-3p, osa-miR167e-3p and their respective targets, coding for heat shock activators and repressors, showed differential expression between primed and non-primed plants. These findings were further validated by qRT-PCR. The results indicate that the miR-regulated heat shock proteins (HSPs)/heat shock transcription factors (HSFs) may serve as important regulatory nodes which are induced during thermo-priming for plant survival and development under high temperatures. Full article
(This article belongs to the Special Issue Research Advances in Plant Genomics)
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12 pages, 1352 KiB  
Article
Full-Length Transcriptome Sequencing Provides Insights into Flavonoid Biosynthesis in Fritillaria hupehensis
by Kunyuan Guo, Jie Chen, Yan Niu and Xianming Lin
Life 2021, 11(4), 287; https://doi.org/10.3390/life11040287 - 28 Mar 2021
Cited by 15 | Viewed by 2769
Abstract
One of the most commonly utilized medicinal plants in China is Fritillaria hupehensis (Hsiao et K.C. Hsia). However, due to a lack of genomic resources, little is known about the biosynthesis of relevant compounds, particularly the flavonoid biosynthesis pathway. A PacBio RS II [...] Read more.
One of the most commonly utilized medicinal plants in China is Fritillaria hupehensis (Hsiao et K.C. Hsia). However, due to a lack of genomic resources, little is known about the biosynthesis of relevant compounds, particularly the flavonoid biosynthesis pathway. A PacBio RS II sequencing generated a total of 342,044 reads from the bulb, leaf, root, and stem, of which 316,438 were full-length (FL) non-redundant reads with an average length of 1365 bp and a N50 of 1888 bp. There were also 38,607 long non-coding RNAs and 7914 simple sequence repeats detected. To improve our understanding of processes implicated in regulating secondary metabolite biosynthesis in F. hupehensis tissues, we evaluated potential metabolic pathways. Overall, this study provides a repertoire of FL transcripts in F. hupehensis for the first time, and it will be a valuable resource for marker-assisted breeding and research into bioactive compounds for medicinal and pharmacological applications. Full article
(This article belongs to the Special Issue Research Advances in Plant Genomics)
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19 pages, 3250 KiB  
Article
Transcriptomic Analysis of the Anthocyanin Biosynthetic Pathway Reveals the Molecular Mechanism Associated with Purple Color Formation in Dendrobium Nestor
by Xueqiang Cui, Jieling Deng, Changyan Huang, Xuan Tang, Xianmin Li, Xiuling Li, Jiashi Lu and Zibin Zhang
Life 2021, 11(2), 113; https://doi.org/10.3390/life11020113 - 2 Feb 2021
Cited by 15 | Viewed by 3395
Abstract
Dendrobium nestor is a famous orchid species in the Orchidaceae family. There is a diversity of flower colorations in the Dendrobium species, but knowledge of the genes involved and molecular mechanism underlying the flower color formation in D. nestor is less studied. Therefore, [...] Read more.
Dendrobium nestor is a famous orchid species in the Orchidaceae family. There is a diversity of flower colorations in the Dendrobium species, but knowledge of the genes involved and molecular mechanism underlying the flower color formation in D. nestor is less studied. Therefore, we performed transcriptome profiling using Illumina sequencing to facilitate thorough studies of the purple color formation in petal samples collected at three developmental stages, namely—flower bud stage (F), half bloom stage (H), and full bloom stage (B) in D. nestor. In addition, we identified key genes and their biosynthetic pathways as well as the transcription factors (TFs) associated with purple flower color formation. We found that the phenylpropanoid–flavonoid–anthocyanin biosynthesis genes such as phenylalanine ammonia lyase, chalcone synthase, anthocyanidin synthase, and UDP-flavonoid glucosyl transferase, were largely up-regulated in the H and B samples as compared to the F samples. This upregulation might partly account for the accumulation of anthocyanins, which confer the purple coloration in these samples. We further identified several differentially expressed genes related to phytohormones such as auxin, ethylene, cytokinins, salicylic acid, brassinosteroid, and abscisic acid, as well as TFs such as MYB and bHLH, which might play important roles in color formation in D. nestor flower. Sturdy upregulation of anthocyanin biosynthetic structural genes might be a potential regulatory mechanism in purple color formation in D. nestor flowers. Several TFs were predicted to regulate the anthocyanin genes through a K-mean clustering analysis. Our study provides valuable resource for future studies to expand our understanding of flower color development mechanisms in D. nestor. Full article
(This article belongs to the Special Issue Research Advances in Plant Genomics)
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17 pages, 3819 KiB  
Article
Haploid Embryogenesis in Isolated Microspore Culture of Carrots (Daucus carota L.)
by Natalia Shmykova, Elena Domblides, Tatiana Vjurtts and Arthur Domblides
Life 2021, 11(1), 20; https://doi.org/10.3390/life11010020 - 31 Dec 2020
Cited by 12 | Viewed by 3569
Abstract
The process of embryogenesis in isolated microspore culture was studied in eight carrot accessions of different origin. The ½NLN-13 medium supplemented with 0.2 mg/L 2,4D and 0.2mg/L kinetin was used to induce embryogenesis. The temperature treatment was performed at 5–6 °C for three [...] Read more.
The process of embryogenesis in isolated microspore culture was studied in eight carrot accessions of different origin. The ½NLN-13 medium supplemented with 0.2 mg/L 2,4D and 0.2mg/L kinetin was used to induce embryogenesis. The temperature treatment was performed at 5–6 °C for three days, followed by cultivation at 25 °C in darkness. As was shown, the first embryogenesis was only observed in microspores at the late vacuolated stage when the nucleus moved from the center to one pole following the long cell axis. Depending on the nucleus position, the microspore can divide into two equal or two different sized cells. Following divisions occurred either in one of these cells or in two. However, microspores that divided into two unequal cells were morphologically different form bi-cellular pollen grain. Embryogenic divisions in bi-cellular pollen grains were not observed. First divisions began by the third day of cultivation, and continued until the globular embryoid stage that was well-seen after the fourth week of cultivation. The already-formed embryoids can develop the secondary embryoids on their surface. Depending on the genotype, up to 1000 secondary embryoids can be produced from one embryoid in the liquid MSm medium supplemented with 0.1 mg/L of kinetin for regeneration. All carrot accessions studied were split into three groups: responsive genotypes, weakly responsive genotypes, and reluctant genotypes. The highest yield was 53 initial embryoids per a 6 cm diameter petri dish. Thus, the Nantskaya 4 cultivar totally produced 256 initial embryoids, out of which 94 developed into green plantlets and 162 into albino plantlets, whereas 97 initial embryoids with 45 albino plantlets formed from them were obtained from Chantenay cultivar. Full article
(This article belongs to the Special Issue Research Advances in Plant Genomics)
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Review

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19 pages, 2462 KiB  
Review
Compendium of Plant-Specific CRISPR Vectors and Their Technical Advantages
by Anshu Alok, Hanny Chauhan, Santosh Kumar Upadhyay, Ashutosh Pandey, Jitendra Kumar and Kashmir Singh
Life 2021, 11(10), 1021; https://doi.org/10.3390/life11101021 - 28 Sep 2021
Cited by 31 | Viewed by 5897
Abstract
CRISPR/Cas mediated genome editing is a revolutionary approach for manipulating the plant genome. However, the success of this technology is highly dependent on selection of a specific vector and the other components. A plant-specific CRISPR/Cas vector usually consists of a Cas gene, target-specific [...] Read more.
CRISPR/Cas mediated genome editing is a revolutionary approach for manipulating the plant genome. However, the success of this technology is highly dependent on selection of a specific vector and the other components. A plant-specific CRISPR/Cas vector usually consists of a Cas gene, target-specific gRNA, leader sequence, selectable marker gene, precise promoters, and other accessories. It has always been challenging to select the specific vector for each study due to a lack of comprehensive information on CRISPR vectors in one place. Herein, we have discussed every technical aspect of various important elements that will be highly useful in vector selection and efficient editing of the desired plant genome. Various factors such as the promoter regulating the expression of Cas and gRNA, gRNA size, Cas variants, multicistronic gRNA, and vector backbone, etc. influence transformation and editing frequency. For example, the use of polycistronic tRNA-gRNA, and Csy4-gRNA has been documented to enhance the editing efficiency. Similarly, the selection of an efficient selectable marker is also a very important factor. Information on the availability of numerous variants of Cas endonucleases, such as Cas9, Cas12a, Cas12b, Casɸ, and CasMINI, etc., with diverse recognition specificities further broadens the scope of editing. The development of chimeric proteins such as Cas fused to cytosine or adenosine deaminase domain and modified reverse transcriptase using protein engineering enabled base and prime editing, respectively. In addition, the newly discovered Casɸ and CasMINI would increase the scope of genetic engineering in plants by being smaller Cas variants. All advancements would contribute to the development of various tools required for gene editing, targeted gene insertion, transcriptional activation/suppression, multiplexing, prime editing, base editing, and gene tagging. This review will serve as an encyclopedia for plant-specific CRISPR vectors and will be useful for researchers. Full article
(This article belongs to the Special Issue Research Advances in Plant Genomics)
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34 pages, 5672 KiB  
Review
Advances in Cereal Crop Genomics for Resilience under Climate Change
by Tinashe Zenda, Songtao Liu, Anyi Dong and Huijun Duan
Life 2021, 11(6), 502; https://doi.org/10.3390/life11060502 - 29 May 2021
Cited by 27 | Viewed by 7917
Abstract
Adapting to climate change, providing sufficient human food and nutritional needs, and securing sufficient energy supplies will call for a radical transformation from the current conventional adaptation approaches to more broad-based and transformative alternatives. This entails diversifying the agricultural system and boosting productivity [...] Read more.
Adapting to climate change, providing sufficient human food and nutritional needs, and securing sufficient energy supplies will call for a radical transformation from the current conventional adaptation approaches to more broad-based and transformative alternatives. This entails diversifying the agricultural system and boosting productivity of major cereal crops through development of climate-resilient cultivars that can sustainably maintain higher yields under climate change conditions, expanding our focus to crop wild relatives, and better exploitation of underutilized crop species. This is facilitated by the recent developments in plant genomics, such as advances in genome sequencing, assembly, and annotation, as well as gene editing technologies, which have increased the availability of high-quality reference genomes for various model and non-model plant species. This has necessitated genomics-assisted breeding of crops, including underutilized species, consequently broadening genetic variation of the available germplasm; improving the discovery of novel alleles controlling important agronomic traits; and enhancing creation of new crop cultivars with improved tolerance to biotic and abiotic stresses and superior nutritive quality. Here, therefore, we summarize these recent developments in plant genomics and their application, with particular reference to cereal crops (including underutilized species). Particularly, we discuss genome sequencing approaches, quantitative trait loci (QTL) mapping and genome-wide association (GWAS) studies, directed mutagenesis, plant non-coding RNAs, precise gene editing technologies such as CRISPR-Cas9, and complementation of crop genotyping by crop phenotyping. We then conclude by providing an outlook that, as we step into the future, high-throughput phenotyping, pan-genomics, transposable elements analysis, and machine learning hold much promise for crop improvements related to climate resilience and nutritional superiority. Full article
(This article belongs to the Special Issue Research Advances in Plant Genomics)
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20 pages, 1540 KiB  
Review
Noncoding RNA: An Insight into Chloroplast and Mitochondrial Gene Expressions
by Asha Anand and Gopal Pandi
Life 2021, 11(1), 49; https://doi.org/10.3390/life11010049 - 13 Jan 2021
Cited by 19 | Viewed by 7516
Abstract
Regulation of gene expression in any biological system is a complex process with many checkpoints at the transcriptional, post-transcriptional and translational levels. The control mechanism is mediated by various protein factors, secondary metabolites and a newly included regulatory member, i.e., noncoding RNAs (ncRNAs). [...] Read more.
Regulation of gene expression in any biological system is a complex process with many checkpoints at the transcriptional, post-transcriptional and translational levels. The control mechanism is mediated by various protein factors, secondary metabolites and a newly included regulatory member, i.e., noncoding RNAs (ncRNAs). It is known that ncRNAs modulate the mRNA or protein profiles of the cell depending on the degree of complementary and context of the microenvironment. In plants, ncRNAs are essential for growth and development in normal conditions by controlling various gene expressions and have emerged as a key player to guard plants during adverse conditions. In order to have smooth functioning of the plants under any environmental pressure, two very important DNA-harboring semi-autonomous organelles, namely, chloroplasts and mitochondria, are considered as main players. These organelles conduct the most crucial metabolic pathways that are required to maintain cell homeostasis. Thus, it is imperative to explore and envisage the molecular machineries responsible for gene regulation within the organelles and their coordination with nuclear transcripts. Therefore, the present review mainly focuses on ncRNAs origination and their gene regulation in chloroplasts and plant mitochondria. Full article
(This article belongs to the Special Issue Research Advances in Plant Genomics)
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